# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:44:19 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3S)-1-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N-[(3,5-dichlorophenyl)methyl]piperidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(CN[C@H]2CCCN(C2)c3[nH]c4ccc(Cl)nc4n3)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 N56  N56  (3S)-1-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N-[(3,5-dichlorophenyl)methyl]piperidin-3-amine  ligand  44  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N56
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 N56  CL2  CL  CL    0  -0.107  -0.2986   2.2511  -2.2412
 N56  C16  C   CR6   0  -0.029  -1.5838   1.7624  -1.1891
 N56  C17  C   CR16  0  -0.196  -2.7738   2.4710  -1.1977
 N56  C    C   CR6   0  -0.028  -3.7712   2.0520  -0.3302
 N56  CL   CL  CL    0  -0.118  -5.2725   2.9153  -0.3071
 N56  C15  C   CR16  0  -0.256  -1.3834   0.6747  -0.3566
 N56  C2   C   CR6   0   0.052  -2.3948   0.2757   0.5103
 N56  C1   C   CR16  0  -0.257  -3.5974   0.9755   0.5230
 N56  C3   C   CH2   0  -0.288  -2.2092  -0.9177   1.4142
 N56  N    N   NH1   0  -0.609  -0.8100  -1.1743   1.6465
 N56  C4   C   CH1   0  -0.058  -0.4620  -2.3391   2.4375
 N56  C8   C   CH2   0  -0.359   1.0682  -2.4066   2.5019
 N56  N1   N   NT    0  -0.490   1.6257  -2.6281   1.1768
 N56  C7   C   CH2   0  -0.356   1.1651  -3.8684   0.5723
 N56  C6   C   CH2   0  -0.426  -0.3535  -3.9018   0.4533
 N56  C5   C   CH2   0  -0.482  -0.9850  -3.6345   1.8159
 N56  C9   C   CR5   0   0.758   1.9549  -1.5577   0.4301
 N56  N4   N   NR15  0  -0.751   2.0847  -1.6129  -0.9292
 N56  C14  C   CR56  0   0.265   2.4816  -0.3680  -1.3490
 N56  C10  C   CR56  0   0.286   2.5629   0.3928  -0.1646
 N56  N2   N   N     0  -0.533   2.2414  -0.3622   0.9164
 N56  C13  C   CR16  0  -0.212   2.7767   0.1959  -2.5664
 N56  C12  C   CR16  0  -0.288   3.1455   1.5405  -2.5464
 N56  C11  C   CR6   0   0.119   3.1840   2.1971  -1.3241
 N56  N3   N   N     0  -0.426   2.9113   1.6721  -0.1503
 N56  CL1  CL  CL    0  -0.138   3.6380   3.8819  -1.3116
 N56  H1   H   HCR6  0   0.298  -2.9172   3.3205  -1.8501
 N56  H2   H   HCR6  0   0.294  -0.4456   0.1383  -0.3713
 N56  H3   H   HCR6  0   0.276  -4.3912   0.6827   1.1984
 N56  H4   H   HCH2  0   0.224  -2.7944  -0.7667   2.3341
 N56  H5   H   HCH2  0   0.256  -2.6548  -1.7824   0.9144
 N56  H6   H   HNH1  0   0.352  -0.3827  -0.3559   2.0620
 N56  H8   H   HCH1  0   0.224  -0.8353  -2.2736   3.4720
 N56  H9   H   HCH2  0   0.274   1.4868  -1.4951   2.9255
 N56  H10  H   HCH2  0   0.258   1.3717  -3.2360   3.1455
 N56  H11  H   HCH2  0   0.257   1.6526  -4.0424  -0.3863
 N56  H12  H   HCH2  0   0.259   1.5000  -4.6831   1.2206
 N56  H13  H   HCH2  0   0.234  -0.6857  -3.1602  -0.2772
 N56  H14  H   HCH2  0   0.243  -0.6600  -4.8802   0.0781
 N56  H15  H   HCH2  0   0.238  -0.7369  -4.4524   2.4997
 N56  H16  H   HCH2  0   0.252  -2.0743  -3.6320   1.7453
 N56  H17  H   HNR5  0   0.424   1.9091  -2.4024  -1.5280
 N56  H19  H   HCR6  0   0.282   2.7278  -0.3548  -3.4961
 N56  H20  H   HCR6  0   0.281   3.3897   2.0594  -3.4613

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 N56  CL1  C11  single    1.745  0.020  1.745
 N56  C11  C12  aromatic  1.388  0.020  1.388
 N56  C11  N3   aromatic  1.314  0.020  1.314
 N56  C12  C13  aromatic  1.394  0.020  1.394
 N56  N3   C10  aromatic  1.326  0.020  1.326
 N56  C13  C14  aromatic  1.374  0.020  1.374
 N56  C10  C14  aromatic  1.410  0.020  1.410
 N56  C10  N2   aromatic  1.357  0.020  1.357
 N56  C14  N4   aromatic  1.372  0.020  1.372
 N56  N2   C9   aromatic  1.322  0.020  1.322
 N56  N4   C9   aromatic  1.367  0.020  1.367
 N56  C9   N1   single    1.346  0.020  1.346
 N56  N1   C7   single    1.455  0.020  1.455
 N56  N1   C8   single    1.455  0.020  1.455
 N56  C7   C6   single    1.524  0.020  1.524
 N56  C8   C4   single    1.533  0.020  1.533
 N56  C6   C5   single    1.525  0.020  1.525
 N56  C4   C5   single    1.529  0.020  1.529
 N56  C4   N    single    1.450  0.020  1.450
 N56  N    C3   single    1.441  0.020  1.441
 N56  C3   C2   single    1.509  0.020  1.509
 N56  C2   C15  aromatic  1.391  0.020  1.391
 N56  C2   C1   aromatic  1.391  0.020  1.391
 N56  C15  C16  aromatic  1.384  0.020  1.384
 N56  C1   C    aromatic  1.385  0.020  1.385
 N56  C16  CL2  single    1.731  0.020  1.731
 N56  C16  C17  aromatic  1.385  0.020  1.385
 N56  C    C17  aromatic  1.387  0.020  1.387
 N56  C    CL   single    1.732  0.020  1.732
 N56  C17  H1   single    0.930  0.020  1.080
 N56  C15  H2   single    0.930  0.020  1.080
 N56  C1   H3   single    0.930  0.020  1.080
 N56  C3   H4   single    0.970  0.020  1.090
 N56  C3   H5   single    0.970  0.020  1.090
 N56  N    H6   single    0.890  0.020  1.040
 N56  C4   H8   single    0.970  0.020  1.090
 N56  C8   H9   single    0.970  0.020  1.090
 N56  C8   H10  single    0.970  0.020  1.090
 N56  C7   H11  single    0.970  0.020  1.090
 N56  C7   H12  single    0.970  0.020  1.090
 N56  C6   H13  single    0.970  0.020  1.090
 N56  C6   H14  single    0.970  0.020  1.090
 N56  C5   H15  single    0.970  0.020  1.090
 N56  C5   H16  single    0.970  0.020  1.090
 N56  N4   H17  single    0.860  0.020  1.020
 N56  C13  H19  single    0.930  0.020  1.080
 N56  C12  H20  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 N56  C15  C16  C17  122.01  3.000
 N56  C17  C16  CL2  119.32  3.000
 N56  C15  C16  CL2  118.67  3.000
 N56  H1   C17  C    121.31  3.000
 N56  H1   C17  C16  121.33  3.000
 N56  C    C17  C16  117.36  3.000
 N56  C1   C    CL   119.22  3.000
 N56  CL   C    C17  118.76  3.000
 N56  C1   C    C17  122.01  3.000
 N56  H2   C15  C2   119.82  3.000
 N56  H2   C15  C16  120.50  3.000
 N56  C2   C15  C16  119.67  3.000
 N56  C3   C2   C1   119.92  3.000
 N56  C1   C2   C15  119.34  3.000
 N56  C3   C2   C15  120.73  3.000
 N56  H3   C1   C2   120.23  3.000
 N56  H3   C1   C    120.17  3.000
 N56  C2   C1   C    119.60  3.000
 N56  H5   C3   H4   105.89  3.000
 N56  H5   C3   N    109.17  3.000
 N56  H4   C3   N    113.95  3.000
 N56  H5   C3   C2   107.55  3.000
 N56  H4   C3   C2   109.08  3.000
 N56  N    C3   C2   110.91  3.000
 N56  H6   N    C4   108.91  3.000
 N56  H6   N    C3   109.39  3.000
 N56  C4   N    C3   117.63  3.000
 N56  H8   C4   C5   108.43  3.000
 N56  H8   C4   C8   107.54  3.000
 N56  C5   C4   C8   108.74  3.000
 N56  H8   C4   N    112.52  3.000
 N56  C5   C4   N    112.12  3.000
 N56  C8   C4   N    107.32  3.000
 N56  H10  C8   H9   107.43  3.000
 N56  H10  C8   N1   108.33  3.000
 N56  H9   C8   N1   109.54  3.000
 N56  H10  C8   C4   109.59  3.000
 N56  H9   C8   C4   111.30  3.000
 N56  N1   C8   C4   110.55  3.000
 N56  C9   N1   C7   121.67  3.000
 N56  C7   N1   C8   112.77  3.000
 N56  C9   N1   C8   118.56  3.000
 N56  H12  C7   H11  105.41  3.000
 N56  H12  C7   C6   109.59  3.000
 N56  H11  C7   C6   111.95  3.000
 N56  H12  C7   N1   106.97  3.000
 N56  H11  C7   N1   111.11  3.000
 N56  C6   C7   N1   111.51  3.000
 N56  H14  C6   H13  107.05  3.000
 N56  H14  C6   C5   110.35  3.000
 N56  H13  C6   C5   110.63  3.000
 N56  H14  C6   C7   109.04  3.000
 N56  H13  C6   C7   109.90  3.000
 N56  C5   C6   C7   109.82  3.000
 N56  H16  C5   H15  105.56  3.000
 N56  H16  C5   C6   110.84  3.000
 N56  H15  C5   C6   109.47  3.000
 N56  H16  C5   C4   111.45  3.000
 N56  H15  C5   C4   107.55  3.000
 N56  C6   C5   C4   111.72  3.000
 N56  N2   C9   N4   112.45  3.000
 N56  N4   C9   N1   122.88  3.000
 N56  N2   C9   N1   124.62  3.000
 N56  H17  N4   C14  125.46  3.000
 N56  H17  N4   C9   127.37  3.000
 N56  C14  N4   C9   107.16  3.000
 N56  C13  C14  C10  120.70  3.000
 N56  C10  C14  N4   104.43  3.000
 N56  C13  C14  N4   134.87  3.000
 N56  N3   C10  N2   126.18  3.000
 N56  N2   C10  C14  110.81  3.000
 N56  N3   C10  C14  123.01  3.000
 N56  C10  N2   C9   105.15  3.000
 N56  H19  C13  C12  121.02  3.000
 N56  H19  C13  C14  122.89  3.000
 N56  C12  C13  C14  116.10  3.000
 N56  H20  C12  C11  120.84  3.000
 N56  H20  C12  C13  120.73  3.000
 N56  C11  C12  C13  118.43  3.000
 N56  CL1  C11  N3   115.68  3.000
 N56  N3   C11  C12  126.27  3.000
 N56  CL1  C11  C12  118.05  3.000
 N56  C11  N3   C10  115.49  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 N56  CONST_01  C1   C2   C15  C16     0.00   0.0  0
 N56  CONST_02  C1   C    C17  C16     0.00   0.0  0
 N56  CONST_03  C2   C15  C16  C17     0.00   0.0  0
 N56  CONST_04  C2   C1   C    C17     0.00   0.0  0
 N56  CONST_05  C15  C2   C1   C       0.00   0.0  0
 N56  CONST_06  C15  C16  C17  C       0.00   0.0  0
 N56  CONST_07  N3   C10  N2   C9    180.00   0.0  0
 N56  CONST_08  C14  C10  N2   C9      0.00   0.0  0
 N56  CONST_09  C13  C14  N4   C9    180.00   0.0  0
 N56  CONST_10  C10  C14  N4   C9      0.00   0.0  0
 N56  CONST_11  C12  C13  C14  N4    180.00   0.0  0
 N56  CONST_12  N3   C10  C14  N4    180.00   0.0  0
 N56  CONST_13  N2   C10  C14  N4      0.00   0.0  0
 N56  CONST_14  C10  N2   C9   N4      0.00   0.0  0
 N56  CONST_15  C11  C12  C13  C14     0.00   0.0  0
 N56  CONST_16  C11  N3   C10  C14     0.00   0.0  0
 N56  CONST_17  N2   C9   N4   C14     0.00   0.0  0
 N56  CONST_18  C12  C11  N3   C10     0.00   0.0  0
 N56  CONST_19  C12  C13  C14  C10     0.00   0.0  0
 N56  CONST_20  C11  N3   C10  N2    180.00   0.0  0
 N56  CONST_21  C13  C14  C10  N2    180.00   0.0  0
 N56  CONST_22  N3   C11  C12  C13     0.00   0.0  0
 N56  CONST_23  N3   C10  C14  C13     0.00   0.0  0
 N56  CONST_24  C10  N2   C9   N1    180.00   0.0  0
 N56  CONST_25  C14  N4   C9   N1    180.00   0.0  0
 N56  CONST_26  C2   C15  C16  CL2   180.00   0.0  0
 N56  CONST_27  C    C17  C16  CL2   180.00   0.0  0
 N56  CONST_28  C3   C2   C15  C16   180.00   0.0  0
 N56  CONST_29  CL   C    C17  C16   180.00   0.0  0
 N56  CONST_30  C3   C2   C1   C     180.00   0.0  0
 N56  CONST_31  C2   C1   C    CL    180.00   0.0  0
 N56  CONST_32  CL1  C11  N3   C10   180.00   0.0  0
 N56  CONST_33  CL1  C11  C12  C13   180.00   0.0  0
 N56  CONST_34  H2   C15  C16  C17   180.00   0.0  0
 N56  CONST_35  H3   C1   C    C17   180.00   0.0  0
 N56  CONST_36  H1   C17  C16  C15   180.00   0.0  0
 N56  CONST_37  H17  N4   C9   N1      0.00   0.0  0
 N56  CONST_38  H19  C13  C14  N4      0.00   0.0  0
 N56  CONST_39  H20  C12  C13  C14   180.00   0.0  0
 N56  Var_01    C9   N1   C8   C4     91.26  30.0  1
 N56  Var_02    C7   C6   C5   C4     53.76  30.0  1
 N56  Var_03    N2   C9   N1   C8     23.82  30.0  3
 N56  Var_04    C6   C7   N1   C8     58.40  30.0  1
 N56  Var_05    C5   C6   C7   N1    -54.05  30.0  1
 N56  Var_06    N    C3   C2   C15    23.41  30.0  2
 N56  Var_07    C4   N    C3   C2   -176.58  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 N56  chir_01  C4  C8  C5  N  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 N56  plan-1  CL2  0.020
 N56  plan-1  C16  0.020
 N56  plan-1  C17  0.020
 N56  plan-1  C    0.020
 N56  plan-1  CL   0.020
 N56  plan-1  C15  0.020
 N56  plan-1  C2   0.020
 N56  plan-1  C1   0.020
 N56  plan-1  C3   0.020
 N56  plan-1  H1   0.020
 N56  plan-1  H2   0.020
 N56  plan-1  H3   0.020
 N56  plan-2  N1   0.020
 N56  plan-2  C9   0.020
 N56  plan-2  N4   0.020
 N56  plan-2  C14  0.020
 N56  plan-2  C10  0.020
 N56  plan-2  N2   0.020
 N56  plan-2  C13  0.020
 N56  plan-2  C12  0.020
 N56  plan-2  C11  0.020
 N56  plan-2  N3   0.020
 N56  plan-2  CL1  0.020
 N56  plan-2  H17  0.020
 N56  plan-2  H19  0.020
 N56  plan-2  H20  0.020

